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United States Department of Agriculture

Agricultural Research Service

Research Project: Exotic and Emerging Plant Diseases of Horticultural Crops

Location: Horticultural Crops Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Node position influences viability and contamination in hazelnut shoot - (Peer Reviewed Journal)

Microbe-ID: An open source toolbox for microbial genotyping and species identification - (Peer Reviewed Journal)
Tabima, J.F., Everhart, S.E., Larsen, M.M., Weisberg, A.J., Kamvar, Z.N., Tancos, M.A., Smart, C.D., Chang, J.H., Grunwald, N.J. 2016. Microbe-ID: An open source toolbox for microbial genotyping and species identification. PeerJ. 4:e2279. doi: 10.7717/peerj.2279.

Early detection of airborne inoculum of Magnaporthe oryzae in turfgrass fields using a quantitative LAMP assay - (Peer Reviewed Journal)
Villari, C., Mahaffee, W.F., Mitchell, T.K., Pedley, K.F., Pieck, M.L., Peduto Hand, F. 2016. Early detection of airborne inoculum of Magnaporthe oryzae in turfgrass fields using a quantitative LAMP assay. Plant Disease. doi: 10.1094/PDIS-06-16-0834-RE.

Gall-ID: Tools for genotyping gall-causing phytopathogenic bacteria - (Peer Reviewed Journal)
Davis, E.W., Weisberg, A.J., Tabima, J., Grunwald, N.J., Chang, J.H. 2016. Gall-ID: Tools for genotyping gall-causing phytopathogenic bacteria. PeerJ. 4:e2222. doi: 10.7717/peerj.2222.

Numerical considerations for Lagrangian stochastic dispersion models: Eliminating rogue trajectories, and the importance of numerical accuracy - (Peer Reviewed Journal)
Bailey, B.N. 2016. Numerical considerations for Lagrangian stochastic dispersion models: Eliminating rogue trajectories, and the importance of numerical accuracy. Journal of Fluid Mechanics. doi: 10.1007/s10546-016-0181-6.

Genomic analyses of dominant U.S. clonal lineages of Phytophthora infestans reveals a shared common ancestry for clonal lineages US11 and US18 and a lack of recently shared ancestry among all other U.S. lineages - (Peer Reviewed Journal)
Knaus, B.J., Tabima, J.F., Davis, C.E., Judelson, H.S., Grunwald, N.J. 2016. Genomic analyses of dominant U.S. clonal lineages of Phytophthora infestans reveals a shared common ancestry for clonal lineages US11 and US18 and a lack of recently shared ancestry among all other U.S. lineages. Phytopathology. doi: 10.1094/PHYTO-10-15-0279-R.

Antimicrobial stewardship through a one health lens: Observations from Washington State - (Peer Reviewed Journal)
D'Angeli, M., Baker, J., Call, D., Davis, M., Kauber, K., Malhotra, U., Matsuura, G., Moore, D., Porter, C., Pottinger, P., Stockwell, V.O., Wagner, C., Wohrle, R., Yoder, J., Yoke, L., Rabinowitz, P. 2016. Antimicrobial stewardship through a one health lens: Observations from Washington State. International Journal of Health Governance Information. 21(3):114-130. doi: 10.1108/IJHG-02-2016-0009.

Population genomics of fungal and oomycete pathogens - (Review Article)
Grunwald, N.J., Mcdonald, B.A., Milgroom, M.G. 2016. Population genomics of fungal and oomycete pathogens. Annual Review of Phytopathology. 54:323-346. doi: 10.1146/annurev-phyto-080614-115913.

VCFR: A package to manipulate and visualize variant call format data in R - (Peer Reviewed Journal)
Knaus, B.J., Grunwald, N.J. 2016. VCFR: A package to manipulate and visualize variant call format data in R. Molecular Ecology Resources. doi: 10.1111/1755-0998.12549.

Developing educational resources for population genetics in R: An open and collaborative approach - (Peer Reviewed Journal)
Kamvar, Z.N., Lopez-Uribe, M.M., Coughlan, S., Grunwald, N.J., Lapp, H., Manel, S. 2016. Developing educational resources for population genetics in R: An open and collaborative approach. Molecular Ecology Resources. doi: 10.1111/1755-0998.12558.

Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum - (Peer Reviewed Journal)
Kasuga, T., Bui, M.Q., Berhardt, E., Swiecki, T., Aram, K., Cano, L.M., Webber, J., Brasier, C., Press, C.M., Grunwald, N.J., Rizzo, D.M., Garbelotto, M. 2016. Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum. BMC Genomics. 17:385. doi: 10.1186/s12864-016-2717-z.

The ebb and flow of airborne pathogens: Monitoring and use in disease management decisions - (Peer Reviewed Journal)
Mahaffee, W.F., Stoll, R. 2016. The ebb and flow of airborne pathogens: Monitoring and use in disease management decisions. Phytopathology. 106(5):420-431. doi: 10.1094/PHYTO-02-16-0060-RVW.

Diverse evolutionary trajectories for small RNA biogenesis genes in the oomycete genus Phytophthora - (Peer Reviewed Journal)
Bollmann, S.R., Fang, Y., Press, C.M., Tyler, B.M., Grunwald, N.J. 2016. Diverse evolutionary trajectories for small RNA biogenesis genes in the oomycete genus Phytophthora. Frontiers in Plant Science. 7:284. doi: 10.3389/fpls.2016.00284.

Loop-mediated isothermal amplification for detection of the tomato and potato late blight pathogen, Phytophthora infestans - (Peer Reviewed Journal)
Hansen, Z.R., Knaus, B.J., Tabima, J.F., Judelson, H.S., Grunwald, N.J., Smart, C.D. 2016. Loop-mediated isothermal amplification for detection of the tomato and potato late blight pathogen, Phytophthora infestans. Journal of Applied Microbiology. 120(4):1010–1020. doi: 10.1111/jam.13079.

SNP-based differentiation of Phytophthora infestans clonal lineages using locked nucleic acid probes and high resolution melt analysis - (Peer Reviewed Journal)
Hansen, Z.R., Knaus, B.J., Tabima, J.F., Press, C.M., Judelson, H.S., Grunwald, N.J., Smart, C.D. 2016. SNP-based differentiation of Phytophthora infestans clonal lineages using locked nucleic acid probes and high resolution melt analysis. Plant Disease. 100(7):1297-1306. doi: 10.1094/PDIS-11-15-1247-RE.

First report of the EU1 clonal lineage of Phytophthora ramorum on tanoak in an Oregon forest - (Peer Reviewed Journal)
Grunwald, N.J., Larsen, M.M., Kamvar, Z.N., Reeser, P.W., Kanaskie, A., Laine, J., Wiese, R. 2016. First report of the EU1 clonal lineage of Phytophthora ramorum on tanoak in an Oregon forest. Plant Disease. 100(5):1024. doi: 10.1094/PDIS-10-15-1169-PDN

An experimental study of momentum and heavy particle transport in a trellised agricultural canopy - (Peer Reviewed Journal)
Miller, N., Stoll, R., Mahaffee, W.F., Neill, T.M., Pardyjak, E.R. 2015. An experimental study of momentum and heavy particle transport in a trellised agricultural canopy. Agriculture and Forest Meterology. 211-212:100-114.

Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality - (Peer Reviewed Journal)
Kamvar, Z.N., Brooks, J.C., Grunwald, N.J. 2015. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Frontiers in Genetics. 6:208. doi: 10.3389/fgene.2015.00208.

Development of a quantitative loop-mediated isothermal amplification (qLAMP) assay for the detection of Magnaporthe oryzae airborne inoculum in turf ecosystems - (Abstract Only)
Villari, C., Mahaffee, W.F., Mitchell, T.K., Pedley, K.F., Pieck, M.L., Peduto Hand, F. 2015. Development of a quantitative loop-mediated isothermal amplification (qLAMP) assay for the detection of Magnaporthe oryzae airborne inoculum in turf ecosystems. In: Poster sessions of the American Phytopathological Society Annual Meeting. August 1-5, 2015, Pasadena, California. 443-P.

Development of a grower performed inoculum detection assay for management of grape powdery mildew - (Peer Reviewed Journal)
Thiessen, L.D., Keune, J.A., Neill, T.M., Turechek, W., Grove, G., Mahaffee, W.F. 2015. Development of a grower performed inoculum detection assay for management of grape powdery mildew. Plant Pathology. 65:238–249. doi: 10.1111/ppa.12421

Five reasons to consider Phytophthora infestans a reemerging pathogen - (Review Article)
Fry, W.E., Birch, P.R., Judelson, H.S., Grunwald, N.J., Danies, G., Everts, K.L., Gevens, A.J., Gugino, B.K., Johnson, D.A., Johnson, S.B., Mcgrath, M.T., Myers, K.L., Ristaino, J.B., Roberts, P.D., Secor, G., Smart, C.D. 2015. Five reasons to consider Phytophthora infestans a reemerging pathogen. Phytopathology. 105:966-981.

Spatial and temporal analysis of populations of the Sudden Oak Death pathogen in Oregon forests - (Peer Reviewed Journal)
Kamvar, Z.N., Larsen, M.M., Kanaskie, A.M., Hansen, E.M., Grunwald, N.J. 2015. Spatial and temporal analysis of populations of the Sudden Oak Death pathogen in Oregon forests. Phytopathology. 105:982-989.

Fungicide sensitivity of US genotypes of Phytophthora infestans (Mont.) de Bary to six oomycete-targeted compounds. - (Peer Reviewed Journal)
Saville, A., Graham, K., Grunwald, N.J., Myers, K., Fry, W.E., Ristaino, J.B. 2015. Fungicide sensitivity of US genotypes of Phytophthora infestans (Mont.) de Bary to six oomycete-targeted compounds. Plant Disease. 99:659-666.

Efficacy of management tools for control of Pythium root rot of Douglas-fir seedlings, 2013 - (Peer Reviewed Journal)
Grunwald, N.J., Press, C.M., Rolfe, K.J., Weiland, G.E., Davis, E.A. 2015. Efficacy of management tools for control of Pythium root rot of Douglas-fir seedlings, 2013. Plant Disease Management Reports. 9:OT004.

The top 10 oomycete pathogens in molecular plant pathology - (Review Article)
Kamoun, S., Furzer, O., Jones, J.D., Judelson, H.S., Ali, G., Dalio, R.J., Roy, S., Schena, L., Zampounis, A., Panabieres, F., Cahill, D., Ruocco, M., Figueirdo, A., Chen, X., Hulvey, J., Stam, R., Lamour, K., Gizen, M., Tyler, B.M., Grunwald, N.J., Tor, M., Mukhtar, S.M., Tome, D., Ackerveken, G., Mcdowell, J., Daayf, F., Fry, W.E., Lindqvist-Kreuze, H., Meijer, H.J., Petre, B., Ristaino, J., Yoshida, K., Birch, P., Govers, F. 2015. The top 10 oomycete pathogens in molecular plant pathology. Molecular Plant Pathology. 16:413:434.

A scalable plant-resolving radiative transfer model based on optimized GPU ray tracing - (Peer Reviewed Journal)
Bailey, B., Overby, M., Willemsen, P., Pardyjak, E.R., Mahaffee, W.F., Stoll, R. 2014. A scalable plant-resolving radiative transfer model based on optimized GPU ray tracing. Agriculture and Forest Meterology. 198-199:192-208. doi.org/10.1016/j.agrformet.2014.08.012.

Real-time PCR assay to distinguish the four Phytophthora ramorum lineages using cellulose binding elicitor lectin (CBEL) locus - (Peer Reviewed Journal)
Gagnon, M.C., Bergeron, M.J., Hamelin, R.C., Grunwald, N.J., Bilodeau, G.J. 2014. Real-time PCR assay to distinguish the four Phytophthora ramorum lineages using cellulose binding elicitor lectin (CBEL) locus. Canadian Journal of Plant Pathology. 36(3):367-376.

Knowing your Phytophthora - (Trade Journal)
Grunwald, N.J. 2014. Knowing your Phytophthora. Digger. 9:33-35.

Effect of vegetative canopy architecture on vertical transport of massless particles - (Peer Reviewed Journal)
Bailey, B.N., Stoll, R., Pardyjak, E.R., Mahaffee, W.F. 2014. Effect of vegetative canopy architecture on vertical transport of massless particles. Atmospheric Environment. 95:480-489.

Lineage, Temperature, and Host Species Have Interacting Effects on Lesion Development in Phytophthora Ramorum - (Peer Reviewed Journal)
Eyre, C.A., Hayden, K.J., Kozanitas, M., Grunwald, N.J., Garbelotto, M. 2014. Lineage, Temperature, and Host Species Have Interacting Effects on Lesion Development in Phytophthora Ramorum. Plant Disease. No. 12: 1717-1727.

Speciation in fungal and oomycete plant pathogens - (Peer Reviewed Journal)
Restrepo, S., Tabima, J.F., Mideros, M.F., Grunwald, N.J., Matute, D.R. 2014. Speciation in fungal and oomycete plant pathogens. Annual Review of Phytopathology. 52:289-316.

The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes - (Peer Reviewed Journal)
Goss, E.M., Tabima, J.F., Cooke, D., Restrepo, S., Fry, W.E., Forbes, G.A., Fieland, V.J., Cardenas, M., Myers, K.L., Grunwald, N.J. 2014. The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes. Proceedings of the National Academy of Sciences. 111(24):8791-8796.

Phytophthora community structure analyses in Oregon nurseries inform systems approaches to disease management - (Peer Reviewed Journal)
Parke, J.L., Fieland, V.J., Lewis, C., Knaus, B.J., Grunwald, N.J. 2014. Phytophthora community structure analyses in Oregon nurseries inform systems approaches to disease management. Phytopathology. 104(10):1052-1062.

Evolution of an experimental population of Phytophthora capsici in the field - (Peer Reviewed Journal)
Dunn, A.R., Bruening, S.R., Grunwald, N.J., Smart, C.D. 2014. Evolution of an experimental population of Phytophthora capsici in the field. Phytopathology. 104(10):1107-1117.

Improving management of grape powdery mildew with new tools and knowledge - (Review Article)
Mahaffee, W.F., Schwebs, S., Hand, F., Gubler, D., Baily, B., Stoll, R. 2014. Improving management of grape powdery mildew with new tools and knowledge. Practical Winery and Vineyards. April:59-67.

Evolution of an experimental population of Phytophthora capsici in the field - (Peer Reviewed Journal)
Dunn, A.R., Bruening, S.R., Grunwald, N.J., Smart, C.D. 2014. Evolution of an experimental population of Phytophthora capsici in the field. Phytopathology. 104(10):1052-1062.

Use of airborne inoculum detection for disease management decisions - (Book / Chapter)
Mahaffee, W.F. 2014. Use of airborne inoculum detection for disease management decisions. In: Gullino, M.L., Bonants, P.J.M., editors. Detection and Diagnostics of Plant Pathogens. New York, NY: Springer. p. 39-54.

Poppr: an R package for genetic analysis of populations with mixed (clonal/sexual) reproduction Reprint Icon - (Peer Reviewed Journal)
Kamvar, Z.N., Tabima, J.F., Grunwald, N.J. 2014. Poppr: an R package for genetic analysis of populations with mixed (clonal/sexual) reproduction. PeerJ. 2:e281.

Phytophthora ramorum - (Book / Chapter)
Everhart, S.E., Tabima, J.F., Grunwald, N.J. 2014. Phytophthora ramorum. In: Dean, R.A. et al. In genomics of plant-associated fungi and oomycetes: Dicot pathogens. Berlin, Germany: Springer Berlin Heidelberg. p. 159-174.

Evolution of RXLR-class effectors in the Oomycete plant pathogen Phytophthora ramorum - (Peer Reviewed Journal)
Goss, E.M., Press, C.M., Grunwald, N.J. 2013. Evolution of RXLR-class effectors in the Oomycete plant pathogen Phytophthora ramorum. PLoS One. 8(11):e79347. doi: 10.1371/journal.pone.0079347.

Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs - (Peer Reviewed Journal)
Fahlgren, N., Bollmann, S.R., Kasschau, K.D., Cuperus, J.T., Press, C.M., Sullivan, C.M., Chapman, E.J., Hoyer, J.S., Gilbert, K.B., Grunwald, N.J., Carrington, J.C. 2013. Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs. PLoS One. 8(10):e77181.

Evidence for multiple introductions and clonality in Spanish populations of Fusarium circinatum - (Peer Reviewed Journal)
Berbegal, M., Perez-Sierra, A., Armengol, J., Grunwald, N.J. 2013. Evidence for multiple introductions and clonality in Spanish populations of Fusarium circinatum. Phytopathology. 103:851-861.

Efficacy of management tools for control of Pythium root rot of Douglas fir seedlings, 2010 - (Peer Reviewed Journal)
Grunwald, N.J., Press, C.M., Rolfe, K.J., Weiland, G.E., Davis, E.A. 2013. Efficacy of management tools for control of Pythium root rot of Douglas fir seedlings, 2010. Plant Disease Management Reports. 7:OT010.

The 2009 late blight pandemic in eastern USA – causes and results - (Review Article)
Fry, W.E., Mcgrath, M.T., Seaman, A., Zitter, T.A., Mcleod, A., Danies, G., Small, I.M., Myers, K., Everts, K., Gevens, A.J., Gugino, B.K., Johnson, S.B., Judelson, H., Ristaino, J., Roberts, P., Secor, G., Seebold, K., Snover-Clift, K., Wyenandt, A., Grunwald, N.J., Smart, C.D. 2013. The 2009 late blight pandemic in eastern USA – causes and results. Plant Disease. 97:296-306.

Eutypa canker and dieback - (Experiment Station)
Mahaffee, W.F., Grove, G. 2013. Eutypa canker and dieback. Pacific Northwest Grape IMP Manual.

The 2009 late blight pandemic in eastern USA - (Review Article)
Fry, W., Mcgrath, M.T., Seaman, A., Zitter, T.A., Mcleod, A., Danies, G., Small, I.M., Myers, K., Everts, K., Gevens, A.J., Gugino, B.K., Johnson, S.B., Judelson, H., Ristaino, J., Roberts, P., Secor, G., Seebold, K., Snover-Clift, K., Wyenandt, A., Grunwald, N.J., Smart, C.D. 2012. The 2009 late blight pandemic in eastern USA. Plant Disease. 97(3):296-306.

Powdery mildew - (Book / Chapter)
Mahaffee, W.F., Glawe, D. 2014. Powdery mildew. In: Linderman, R.G., Benson, D.M., editors. Compendium of Rhododendron and Azalea Diseases and Pests. 2nd edition. St. Paul, MN: The American Phytopathological Society Press. p. 41-44.

Identification of Phytophthora species baited and isolated from forest soil and streams in northwestern Yunnan province, China - (Peer Reviewed Journal)
Huai, W., Tian, G., Hansen, E.M., Zhao, W., Goheen, E.M., Grunwald, N.J., Cheng, C. 2013. Identification of Phytophthora species baited and isolated from forest soil and streams in northwestern Yunnan province, China. Forest Pathology. 43(2):87–103.

Is it tea time? - (Popular Publication)
Mahaffee, W.F. 2012. Is it tea time? Pennsylvania Landscape and Nursery. March/April 2012 Issue.

Last Modified: 2/23/2016
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